I have some general questions about using data linked to the Earth Microbiome Project (EMP).
I will type my concerns and the questions in a list below
I wanted to download some 16S sequenced data from Qiita linked to EMP. I wanted use the EBI-ENA accession number provided in qiita database to download the same data set from the European nucleotide archive (ENA). I want to know if I can access the same data set that is available under a particular qiita-id using the EBI accession that is provided?
I’m asking this because I found that for some projects, the description in ENA is for 18S data sequencing while the ‘data type’ indicated in qiita database is 16S.
Does anyone have any experience using EMP DNA extraction protocol for liquid material?
The protocol that is available in the EMP website (https://www.protocols.io/view/earth-microbiome-project-emp-high-throughput-htp-d-pdmdi46) says to use 250uL of liquid material for DNA extraction. I was wondering if that amount is enough to capture all the microbes represented in a particular sample. Moreover, isn’t filtration through a particular pore size (e.g- 0.22um) required to concentrate the microbes for DNA extraction?
Sorry for the long message. Would be grateful to know what you all think about this.
Any help is much appreciated.
Many thanks in advance!